1RD9 | pdb_00001rd9

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	38% PEG 300, 50 mM NaCl, 100 mM Tris-HCl, and 2.3mM BV2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.983	α = 90
b = 66.072	β = 105.84
c = 77.818	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2003-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0000	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.44	50	92.4	0.083	14.4	3.6	86307	81971		-3	16.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.44	1.5	73.3		0.567	1.9	3.1	6452

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.44	37.53	77876	4090	92.01	0.13394	0.13394	0.13137	0.17	0.18357	0.21	RANDOM	12.551

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.01		-0.02	-0.04		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	19.22
r_scangle_it	7.499
r_sphericity_bonded	7.2
r_dihedral_angle_1_deg	6.976
r_scbond_it	5.667
r_mcangle_it	4.444
r_mcbond_it	3.455
r_rigid_bond_restr	2.48
r_angle_refined_deg	1.464
r_angle_other_deg	0.88
r_nbd_other	0.335
r_symmetry_vdw_refined	0.309
r_symmetry_vdw_other	0.29
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.092
r_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_other	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4079
Nucleic Acid Atoms
Solvent Atoms	491
Heterogen Atoms	163

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
XTALVIEW	refinement